Additional file 1 of An overlooked subset of Cx3cr1wt/wt microglia in the Cx3cr1CreER-Eyfp/wt mouse has a repopulation advantage over Cx3cr1CreER-Eyfp/wt microglia following microglial depletion

Additional file 1: Figure S1. Additional data related to Fig. 1. A Representative 8 sections of Hoechst staining of Cx3cr1CreER-Eyfp/wt mouse brain sequential sagittal slices, the numbers representing the location and number of EYFP��� microglia in that location, each color represents one mouse, n = 6. Figure S2. Morphology analysis. A The process to prepare topological skeleton from the original photomicrographs. The full-size maximum intensity projection images (top) were processed into binary images (middle) and then skeletonized (bottom) following the ImageJ plugin protocol. Cropped images (right) from the original full-size images (left) were shown to improve the visualization. Scale bar, 50 ��m. B The Analyze Skeleton plugin was applied, and skeletonized endpoints were tagged purple, the slab is orange, and the junction is pink. The tagged data are summarized as total length (sum of endpoints, slab, and junction) and the total number of endpoints. C The process area is represented as the convex hull area by connecting the process ends using the ImageJ polygon tool. Figure S3. Additional data related to Fig. 1. A Gating strategies of flow cytometry analyses. B EYFP��� microglia ratio of total microglia at 3 weeks, 4 weeks, 6 weeks, 9 weeks and 15 weeks old mice, n = 4, 4, 6, 4, respectively, mean �� s.d. No significant difference by one-way ANOVA. C UMAP plots from single-cell sequencing, each dot represents one cell, the color represents the expression levels of Cx3cr1. D Histogram plot of Cx3cr1. The x-axis represents Cx3cr1 expression read counts; the y-axis represents cell numbers. Figure S4. Additional data related to Fig. 2. A Graph showing relative Iba-1+ microglia at 1 day, 3 days and 7 days after the final Tam injection, respectively; n = 3���4, mean �� s.d. *p